I rooted my phone (Galaxy Nexus 4.1.1 JRO03C). I am able to access nearly all files under data/data/* folder. However, a few files cannot be opened, such as data/data/com.android.browser/databases/webview.db

I suspect these files are encrypted. Is there any way to decrypt them?

You now will probably argue you said having rooted your device. So far, so fine. But did you use your "root powers" when trying to access those databases? Just having your device rooted does not mean all stuff automatically runs with root permissions (see: Do all applications run as root on my phone after rooting?). The app you're using to open those files must itself have requested (and be granted) root permissions -- or they might get either no or only restricted permissions on files they do not own.